Quantifying force-dependent and zero-force dna intercalation by single-molecule stretching

ABSTRACT We used single DNA molecule stretching to investigate DNA intercalation by ethidium and three ruthenium complexes. By measuring ligand-induced DNA elongation at different ligand

concentrations, we determined the binding constant and site size as a function of force. Both quantities depend strongly on force and, in the limit of zero force, converge to the known bulk

solution values, when available. This approach allowed us to distinguish the intercalative mode of ligand binding from other binding modes and allowed characterization of intercalation with

binding constants ranging over almost six orders of magnitude, including ligands that do not intercalate under experimentally accessible solution conditions. As ligand concentration

increased, the DNA stretching curves saturated at the maximum amount of ligand intercalation. The results showed that the applied force partially relieves normal intercalation constraints.

We also characterized the flexibility of intercalator-saturated dsDNA for the first time. Access through your institution Buy or subscribe This is a preview of subscription content, access

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RESOLUTION Article Open access 19 March 2025 PREDICTING THE EFFECT OF BINDING MOLECULES ON THE SHAPE AND MECHANICAL PROPERTIES OF STRUCTURED DNA ASSEMBLIES Article Open access 31 July 2024

HIGH-THROUGHPUT SINGLE-MOLECULE QUANTIFICATION OF INDIVIDUAL BASE STACKING ENERGIES IN NUCLEIC ACIDS Article Open access 06 February 2023 REFERENCES * Lerman, L.S. Structural considerations

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Med._ 35, 527–533 (2003). Article  CAS  Google Scholar  Download references ACKNOWLEDGEMENTS We acknowledge funding from the US National Science Foundation (MCB0238190), US National

Institutes of Health (GM072462) and American Chemical Society Petroleum Research Fund. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Physics, Northeastern University, Boston,

02115, Massachusetts, USA Ioana D Vladescu, Micah J McCauley & Mark C Williams * Department of Chemistry, Mount Holyoke College, South Hadley, 01075, Massachusetts, USA Megan E Nuñez *

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, 55455, Minnesota, USA Ioulia Rouzina * Center for Interdisciplinary Research on Complex

Systems, Northeastern University, Boston, 02115, Massachusetts, USA Mark C Williams Authors * Ioana D Vladescu View author publications You can also search for this author inPubMed Google

Scholar * Micah J McCauley View author publications You can also search for this author inPubMed Google Scholar * Megan E Nuñez View author publications You can also search for this author

inPubMed Google Scholar * Ioulia Rouzina View author publications You can also search for this author inPubMed Google Scholar * Mark C Williams View author publications You can also search

for this author inPubMed Google Scholar CONTRIBUTIONS I.D.V. performed most experiments. M.J.M. maintained the instrument, labeled DNA and performed some experiments. M.E.N. provided

ruthenium compounds. I.D.V., I.R., M.E.N. and M.C.W. designed the research. I.R. developed the theory. I.D.V., M.E.N., I.R. and M.C.W. wrote the paper. CORRESPONDING AUTHORS Correspondence

to Ioulia Rouzina or Mark C Williams. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIG. 1 Drug effect

on hysteresis behavior. (PDF 92 kb) SUPPLEMENTARY FIG. 2 Dependence of Ru(phen)2dppz2+ binding on force. (PDF 81 kb) SUPPLEMENTARY FIG. 3 Dependence of Ru(phen)32+ binding on force. (PDF 77

kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Vladescu, I., McCauley, M., Nuñez, M. _et al._ Quantifying force-dependent and zero-force DNA

intercalation by single-molecule stretching. _Nat Methods_ 4, 517–522 (2007). https://doi.org/10.1038/nmeth1044 Download citation * Received: 29 January 2007 * Accepted: 21 March 2007 *

Published: 29 April 2007 * Issue Date: June 2007 * DOI: https://doi.org/10.1038/nmeth1044 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get

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